Alignment is a concept that refers to the state of the physical reality as a reflection of Consciousness. When physical reality accurately reflects the will, intent, and desires of Consciousness we say that physical creation is in alignment with Consciousness. When the physical universe is "off" in some way, we say that physical creation is out of alignment or (in severe cases) disjunctive of source Consciousness.
Alignment may refer to the general state of reality, but also to individual behaviour. Our behaviour is aligned when we act in accordance with the will and intent of our own highest Self. It is out of alignment, or disjunctive when we act against the intent and will of Self.
Jainism: Samyaktva or perfection/completion.
The Christian term for alignment is "righteousness" or even "reconciliation" (2 Corinthians 5: 19-20) "He who through faith is righteous (aligned) shall live." Romans 1:15. Several passages in the bible speak to the nature of alignment, including Mathew 5, Mathew 6, and a large swath of Mathew 7
Strict alignment (Mathew 5: 20). Even stricter than before (Mathew 5: 21-26),
Helping the weak Acts 20: 32-35
Mathew 19: 16-22 makes clear what Christ thought the parameters of alignment were.
"Those who belong to Christ Jesus have crucified the flesh" (Galatians 5: 24) meaning that those who are connected leave venal interests and desires behind.
Paul speaks of "righteousness, self control," (Acts, 27: 17) both of which are components of alignment, righteousness being a state of strong moral/behavioural alignment with Consciousness, and self control (i.e. control of the physical vehicle) a basic requirement of incarnated Consciousness. In Acts 10: 34-35 we are told that "...God does not show favoritism but accepts from every nation the one who fears him and does what is right." In this context, doing what is right means doing what is in alignment with your own highest self.
Colossians 3: 12-14. "Therefore, as God’s chosen people, holy and dearly loved, clothe yourselves with compassion, kindness, humility, gentleness and patience. Bear with each other and forgive one another if any of you has a grievance against someone. Forgive as the Lord forgave you. And over all these virtues put on love, which binds them all together in perfect unity"
In Galatians, Paul says that "whoever sows to please the Spirit, from the Spirit will reap eternal life." Translation, "sows to please the Spirit" meaning those who act in alignment Galatians 6: 8-9.
Galatians 5: 13-26 is a short treatise on alignment.
When we achieve alignment, we connect and achieve Salvation. Revelations 22:14 refers to "washing of the robes". "Blessed are those who wash their robes, so that they may have the right to the tree of life, and may enter by the gates into the city." Rev 22:14
When we are aligned, Consciousness recieves us (2 Corinthians 6: 17)
When we are aligned, we are "in step with the Spirit" Galatians 5:25
One who is aligned is perfectly "holy" -> "Let us purify ourselves from everything that contaminates body and spirit, perfecting holiness out of reverence for God" 2 Corinthians 7: 1
Acts of the Flesh a euphemism for misalignment (Galatians 5: 16-18)
Reality is "in alignment" with Consciousness when it is a pure and uncorrupted expression of Consciousness (with a capital "C").
Alignment may refer to the general state of physical reality as a reflection of Consciousness, or it may refer to specific instances/examples of alignment, as for example the alignment of Bodily Ego with Spiritual Ego. In this case, alignment refers to the extent to which the Physical Unit is acting as an “appropriate and responsive” physical unit for Resident Monadic Consciousness. The easiest way to think about this is to think about a car. If you get into a car and you hit the gas, but the car slows down, or if you turn the wheel left, but the car turns right, the car is out of alignment (i.e. unresponsive) to the intent of the driver. It is the same with your physical body. If the RMC that "owns" the Physical Unit wants the Physical Unit to do one thing, but it does another, the body is out of alignment with RMC.
To the extent that the physical unit is functioning as an appropriate and responsive vehicle for the resident monadic consciousness (RMC) we may say that the physical unit is in alignment with its RMC. A physical unit that is in alignment with its own RMC perceives, thinks and acts in accordance with the perceptions, thoughts, and desires of its own RMC (Sosteric, SA1). A physical unit which, because of (for example) Toxic Socialization and Indoctrination, thinks and acts in ways that are against the nature and/or wishes of its RMC, or a physical unit that is unresponsive to the wishes of its RMC, may be said to be out of alignment.
Alignment is a requirement of Connection (see Connection Framework) of the physical unit. A physical unit that is out of alignment may have difficulty with the process of awakening and activation (for more, see LPWKB3).
Acts that the physical unit engages in may be painful to the RMC and therefore the RMC may be forced to remain "at a distance" from the physical unit (thereby lowering the CQ of the physical unit. At the same time, the uncompromising nature of the RMC may cause disjuncture and discomfort in the physical unit and as a result the physical unit may itself push away (i.e., repress) the RMC.
Alignment of the physical unit is a key developmental task. When not attained in childhood, alignment can be attained in adulthood by encouraging the physical unit to engage in right thinking and right action and by providing right environment.
Alignment of the physical unit with Consciousness/God is a common theme in traditional spirituality.
Jainism: Samyaktva is what occurs when a spiritual seeker establishes Samyag Darshan (right perception), Samyag Jnana (right knowledge) and Samyak Charitra (right practice). When perfection/alignment is established, Connection may occur.
Judaism: The Jewish Torah contains extensive and detailed "laws" (i.e. statements of alignment) that God gave Moses indicating how the people were to behave in relation to God/Consciousness, and with each other as well (Ehrman, 2007).
Psychology: Alignment has also been a concern, from time to time, among psychologists. In an 1960 radio interview, Abraham Maslow suggest that there were "basic, underlying, human standards that are cross-cultural" (Maslow, 1961). These standards, which according to Maslow were universal, should be used to govern the social order.
Christ, in the Gospel of Mary Magdalene, discusses alignment in the context of adultry and sin, pointing out that "Sin as such does not exist. You only bring it into manifestation when you act in ways that are adulterous (i.e. out of alignment or disjuctive) in nature."
Alignment is a significant concern of knowledgeable kundalini practitioners. As GM CKS notes, "When the Kundalini is awakened, the positive and negative qualities of the person will be magnified to a very high degree. Kundalini energy is like fertilizer. Whatever seeds are in the ground will be stimulated to grow. So whatever ancient seeds a person possesses, whether good or bad, will be magnified. This is why a person going into the spiritual path experiences intense inner battles. Therefore, it is important to practice inner purification." (Sui, 2016).
Sharp, Michael (BOOK1). Lightning Path Workbook One: Introduction to Authentic Spirituality. Lightning Path Press. 
Sharp, Michael (BOOK2). Lightning Path Workbook Two: Healing. Lightning Path Press. 
Sharp, Michael (BOOK3). Lightning Path Workbook Three: Connection. Lightning Path Press. 
Sharp, Michael (GA). The Great Awakening: Concepts and Techniques for Successful Spiritual Practice.
Bourgeault C. (2015) The Gospel of Mary Magdalene. Parabola. New York.
Ehrman, Bart D. 2007. Misquoting Jesus: The Story Behind Who Changed the Bible and Why: Harper One.
Maslow, Abraham H. 1961. "Eupsychia—The Good Society." Journal of Humanistic Psychology 1 (2):1.
Sui, Choa Kok. 2016. How to Safely Awaken the Kundalini! http://www.awarenessmag.com/julaug1/JA1_SAFELY_AWAKEN.HTML
Sosteric, Mike. (SOA). The Science of Ascension: A Neurologically Grounded, Spiritually Sophisticated Theory of Mystical/Spiritual Experience. Unpublished.